[buster-discuss] defining solvent content - missing part of structure

[Miguel Ortiz Lombardía]

Weird, we also got the software from GlobalPhasing directly.

As for seq2seq, I have no clue, I have never used. Have you tried to
remove the "END" line in your pdb file?

Cheers,


Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Le 07/05/13 11:20, Michael Hothorn a écrit :
> 
> 
> 
> -------- Original Message --------
> Subject: 	Re: [buster-discuss] defining solvent content - missing part
> of structure
> Date: 	Tue, 07 May 2013 11:19:35 +0200
> From: 	Michael Hothorn <michael at hothorn.de>
> To: 	Miguel Ortiz Lombardía <miguel.ortiz-lombardia at afmb.univ-mrs.fr>
> 
> 
> 
> No. I downloaded it from globalphasing directly. The sw just stands for 
> software and holds all my xtal stuff. I managed to get a script to run 
> that is called seq2seq and that generates a TNT file from plain ASCII 
> sequence. I used the ASCII sequence of my entire protein making up the 
> crystal, although I am only providing pdb coordinates for about half of 
> it. That turned out not to be a smart idea:
> 
>  ERROR : [pdb2tnt-0020] unable to get coordinates for
>          residue/linkage "END" - please check your sequence
>          file!
> 
> I guess the TNT file and the pdb file need to match, or am I missing 
> something?
> 
> Is there a way to tell buster that the supplied pdb file make up only 
> about 50% of the scattering mass. As it is the solvent content seems to 
> be calculated based on the supplied pdb file, it is much to high.
> 
> best wishes,
> Michael
> 
> 
> On 05/07/2013 11:01 AM, Miguel Ortiz Lombardía wrote:
>> Hi,
>>
>> At least in our installation the script resides precisely where indicated:
>>
>> $BDG_home/bin/buster/pirToSeq.pl
>>
>> Is your installation from some kind of 'fink' package? (I am guessing
>> from the path that you show, including 'sw') If so, check that the
>> maintainer of the package included all the files.
>>
>> Cheers,
>>
>>
>> Miguel Ortiz Lombardía
>>
>> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
>> CNRS, Aix-Marseille Université
>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
>> Tel: +33(0) 491 82 55 93
>> Fax: +33(0) 491 26 67 20
>> mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr
>> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>>
>> Le 07/05/13 09:59, Michael Hothorn a écrit :
>>> Hi,
>>>
>>> I am trying to refine a partial model: I have a molecular replacement
>>> solution that comprises about 50% of the asymmetric unit and I would
>>> like to specify the scattering mass that is missing in the initial pdb
>>> file to buster. I read in the manual that this can be done by supplying
>>> a TNT sequence file
>>>
>>> $BDG_home/bin/buster/pirToSeq.pl <file.pir>
>>> 		      <file.seq>
>>>
>>>
>>> However, I cannot find the recommended script in my buster 2.10
>>> installation:
>>>
>>> mhothorn at crunchy:/fml/ag-hothorn/share/sw/buster_2.10$ find -name *.pl
>>> ./lib/libmap.pl
>>> ./lib/libxtal.pl
>>> ./lib/libbdg.pl
>>> ./lib/libfloat.pl
>>> ./lib/cryptic.pl
>>> ./lib/cgi-lib.pl
>>> ./lib/libhtml.pl
>>> ./bin/buster/cleanup.pl
>>> ./buffet/lib/libtnt.pl
>>> ./buffet/lib/XfitHelper.pl
>>> ./buffet/lib/libbuster.pl
>>> ./buffet/lib/jos1dHelper.pl
>>> ./buffet/lib/xplot84Helper.pl
>>> ./buffet/lib/jos2dHelper.pl
>>> ./buffet/cgi-bin/save.pl
>>> ./buffet/cgi-bin/deltmp.pl
>>> ./buffet/cgi-bin/delcrd.pl
>>> ./buffet/cgi-bin/changeprefs.pl
>>> ./buffet/cgi-bin/changepass.pl
>>> ./buffet/cgi-bin/index.pl
>>> ./buffet/cgi-bin/createMap.pl
>>> ./buffet/cgi-bin/map.pl
>>> ./buffet/cgi-bin/restart.pl
>>> ./buffet/cgi-bin/delProject.pl
>>> ./buffet/cgi-bin/jos.pl
>>> ./buffet/cgi-bin/dosave.pl
>>> ./buffet/cgi-bin/resume.pl
>>> ./tnt/data/protgeo_eh99_omega_torsion.pl
>>>
>>> Could you please provide advice on how to specify the missing atoms to
>>> buster (so that it assumes the correct solvent content for example).
>>>
>>> Thanks!
>>> Michael
>>> _______________________________________________
>>> buster-discuss mailing list
>>> buster-discuss at globalphasing.com
>>> https://www.globalphasing.com/mailman/listinfo/buster-discuss
>>>
> 
> 
> 
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